The Open Protein Structure Annotation Network
PDB Keyword


    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of predicted HD superfamily hydrolase involved in NAD metabolism (NP_347894.1) from Clostridium acetobutylicum at 1.50 A resolution. To be published
    Site JCSG
    PDB Id 3ccg Target Id 367850
    Molecular Characteristics
    Source Clostridium acetobutylicum atcc 824
    Alias Ids TPS1528,NP_347894.1, BIG_3, 86278 Molecular Weight 21434.34 Da.
    Residues 189 Isoelectric Point 5.55
    Sequence mwsydkitdylmnnlgekrykhslgvmdtavrlagiynedtekariaglvhdcakklpgekiieictne gyelgdedirnsyllhglagrilakkvigiddedvlnaiefhttgrpnmsllekiiyiadyiepgrefk gvdelrkaadedlnkallmsfdntikfvidkggflhhntiearnylisrkg
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.50 Rfree 0.217
    Matthews' coefficent 2.23 Rfactor 0.180
    Waters 198 Solvent Content 44.95

    Ligand Information


    Google Scholar output for 3ccg
    1. Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers
    H Van Den Bedem, A Dhanik, JC Latombe - Section D: Biological , 2009 - scripts.iucr.org
    2. Structural and Biochemical Analysis of Nuclease Domain of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated Protein 3 (Cas3)
    S Mulepati, S Bailey - Journal of Biological Chemistry, 2011 - ASBMB

    Protein Summary

    NP_347894 has been annotated as HD superfamily hydrolase. NP_347894 is a member of COG1713: predicted HD superfamily hydrolase involved in NAD metabolism. Its homologs are often seen in genomic neighborhood, or in fusion with probable nicotinate-nucleotide adenylyltransferase (EC NP_347894 is also similar to PF01966, which is metal-dependent HD superfamily phosphohydrolase.  Sequence alignment also agrees with this function annotation. NP_347894 mainly consists of helix bundles.  The directly superposing comparison between NP_347894 and Dali search results suggests the structurally similar preteins with PDB codes: 2QRT and 2O08. An active site with 2 metal-ion has been characterized. The metal ions are assigned as FE.  The following conserved residues against 2QRT are found: His 22, 51 and 85, Asp 52 and 129, which complexes with the Fe ions in the active site. There is also a formic ion from crystallization condition is also observed near to the active site. Arg 19 and Lsy 55 provide H-Bonding force to phosphate. There is one subunit in each asymmetric unit as a dimer. The surface interacting calculation suggests the biomolecule of NP_347894 should be a dimer.

    Ligand Summary

    Metals: Fe
    Ligands: phosphate ion.





    No references found.

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